Identification and expression analysis of the SQUAMOSA promoter-binding protein (SBP)-box gene family in Prunus mume

Abstract

SQUAMOSA promoter-binding protein (SBP)-box family genes encode plant-specific transcription factors that play crucial roles in plant development, especially flower and fruit development. However, little information on this gene family is available for Prunus mume, an ornamental and fruit tree widely cultivated in East Asia. To explore the evolution of SBP-box genes in Prunus and explore their functions in flower and fruit development, we performed a genome-wide analysis of the SBP-box gene family in P. mume. Fifteen SBP-box genes were identified, and 11 of them contained an miR156 target site. Phylogenetic and comprehensive bioinformatics analyses revealed that different groups of SBP-box genes have undergone different evolutionary processes and varied in their length, structure, and motif composition. Purifying selection has been the main selective constraint on both paralogous and orthologous SBP-box genes. In addition, the sequences of orthologous SBP-box genes did not diverge widely after the split of P. mume and Prunus persica. Expression analysis of P. mume SBP-box genes revealed their diverse spatiotemporal expression patterns. Three duplicated SBP-box genes may have undergone subfunctionalization in Prunus. Most of the SBP-box genes showed high transcript levels in flower buds and young fruit. The four miR156-nontargeted genes were upregulated during fruit ripening. Together, these results provide information about the evolution of SBP-box genes in Prunus. The expression analysis lays the foundation for further research on the functions of SBP-box genes in P. mume and other Prunus species, especially during flower and fruit development.

AGING GENE PATHWAY OF MICRORNAS 156/157 AND 172 IS ALTERED IN JUVENILE AND ADULT PLANTS FROM IN VITRO PROPAGATED Prunus sp.

“…The multiple alignments of SPL-like proteins from peach and Arabidopsis revealed a high degree of conservation in the SBP domains ( Figure S1). Similar results were reported by Xu et al (2015) in P. mume, while the TOE-like proteins with their AP2 domains had the same behavior.…”

“…We searched the homologous genes of the aging pathway, miRNAs 156/157 and 172 and their target genes in P. persica (Figure 1). Homologous genes of the aging pathway are found in the P. persica genome and are expressed in several Prunus species, suggesting that they play a role during developmental transitions in these perennial tree species (Xu et al, 2015). The target genes of miR156 are the SPL genes that control aspects of plant growth and development, including vegetative phase change, flowering time, and the leaf initiation rate (Bergonzi and Albani, 2011).…”

“…In addition, six of the 144 members of the Arabidopsis AP2 family are involved in vegetative phase change and juvenile and adult development (TOE genes). Based on the previous report described by Xu et al (2015) and BLAST, we identified six SPL-like and four TOE-like genes in P. persica, with homology to Arabidopsis SPL and TOE genes involved in vegetative phase change. At the amino acid level, the putative members belonging to the SPL family have similitude percentages ranging from 43.6 to 55.7%, while the putative TOE proteins have amino acid similitude between 35.4 and 46.5% Table 2.…”

“…This aging pathway seems to be conserved in fruit tree species, such as those belonging to the Prunus genus of the Rosaceae family (Xu et al, 2015).…”

“…This protein family is plant specific and is encoded by a large gene family (Cardon et al, 1999). For instance, 16 and 15 SPL genes have been described in A. thaliana and P. mume Siebold & Zucc., respectively (Cardon et al, 1999;Xu et al, 2015).…”